Accurate Automatic Segmentation of Amygdala Subnuclei and Modeling of Uncertainty via Bayesian Fully Convolutional Neural Network

Recent advances in deep learning have improved the segmentation accuracy of subcortical brain structures, which would be useful in neuroimaging studies of many neurological disorders. However, most of the previous deep learning work does not investigate the specific difficulties that exist in segmenting extremely small but important brain regions such as the amygdala and its subregions. To tackle this challenging task, a novel 3D Bayesian fully convolutional neural network was developed to apply a dilated dualpathway approach that retains fine details and utilizes both local and more global contextual information to automatically segment the amygdala and its subregions at high precision. The proposed method provides insights on network design and sampling strategy that target segmentations of small 3D structures. In particular, this study confirms that a large context, enabled by a large field of view, is beneficial for segmenting small objects; furthermore, precise contextual information enabled by dilated convolutions allows for better boundary localization, which is critical for examining the morphology of the structure. In addition, it is demonstrated that the uncertainty information estimated from our network may be leveraged to identify atypicality in data. Our method was compared with two state-of-the-art deep learning models and a traditional multi-atlas approach, and exhibited excellent performance as measured both by Dice overlap as well as average symmetric surface distance. To the best of our knowledge, this work is the first deep learning-based approach that targets the subregions of the amygdala.